OpenSwathWorkflow Class Reference

Class to execute an OpenSwath Workflow. More...

#include <OpenMS/ANALYSIS/OPENSWATH/OpenSwathWorkflow.h>

Inheritance diagram for OpenSwathWorkflow:

Public Member Functions
	OpenSwathWorkflow (bool use_ms1_traces)
void	performExtraction (const std::vector< OpenSwath::SwathMap > &swath_maps, const TransformationDescription trafo, const ChromExtractParams &cp, const Param &feature_finder_param, const OpenSwath::LightTargetedExperiment &transition_exp, FeatureMap &out_featureFile, bool store_features, OpenSwathTSVWriter &tsv_writer, OpenSwathOSWWriter &osw_writer, Interfaces::IMSDataConsumer *chromConsumer, int batchSize, bool load_into_memory)
	Execute the OpenSWATH workflow on a set of SwathMaps and transitions. More...
Public Member Functions inherited from ProgressLogger
	ProgressLogger ()
	Constructor. More...
	~ProgressLogger ()
	Destructor. More...
	ProgressLogger (const ProgressLogger &other)
	Copy constructor. More...
ProgressLogger &	operator= (const ProgressLogger &other)
	Assignment Operator. More...
void	setLogType (LogType type) const
	Sets the progress log that should be used. The default type is NONE! More...
LogType	getLogType () const
	Returns the type of progress log being used. More...
void	startProgress (SignedSize begin, SignedSize end, const String &label) const
	Initializes the progress display. More...
void	setProgress (SignedSize value) const
	Sets the current progress. More...
void	endProgress () const
	Ends the progress display. More...

Protected Member Functions
void	writeOutFeaturesAndChroms_ (std::vector< OpenMS::MSChromatogram > &chromatograms, const FeatureMap &featureFile, FeatureMap &out_featureFile, bool store_features, Interfaces::IMSDataConsumer *chromConsumer)
	Write output features and chromatograms to disk. More...
void	MS1Extraction_ (const std::vector< OpenSwath::SwathMap > &swath_maps, std::map< std::string, OpenSwath::ChromatogramPtr > &ms1_chromatograms, Interfaces::IMSDataConsumer *chromConsumer, const ChromExtractParams &cp, const OpenSwath::LightTargetedExperiment &transition_exp, const TransformationDescription &trafo_inverse, bool load_into_memory, bool ms1only=false)
	Perform MS1 extraction and store result in ms1_chromatograms. More...
void	scoreAllChromatograms (const OpenSwath::SpectrumAccessPtr input, const std::map< std::string, OpenSwath::ChromatogramPtr > &ms1_chromatograms, const std::vector< OpenSwath::SwathMap > swath_maps, OpenSwath::LightTargetedExperiment &transition_exp, const Param &feature_finder_param, TransformationDescription trafo, const double rt_extraction_window, FeatureMap &output, OpenSwathTSVWriter &tsv_writer, OpenSwathOSWWriter &osw_writer, bool ms1only=false)
	Perform scoring on a set of chromatograms. More...
void	selectCompoundsForBatch_ (const OpenSwath::LightTargetedExperiment &transition_exp_used_all, OpenSwath::LightTargetedExperiment &transition_exp_used, int batch_size, size_t j)
	Select which compounds to analyze in the next batch (and copy to output) More...
void	copyBatchTransitions_ (const std::vector< OpenSwath::LightCompound > &used_compounds, const std::vector< OpenSwath::LightTransition > &all_transitions, std::vector< OpenSwath::LightTransition > &output)
	Copy the required transitions to output. More...
void	prepareExtractionCoordinates_ (std::vector< OpenSwath::ChromatogramPtr > &chrom_list, std::vector< ChromatogramExtractorAlgorithm::ExtractionCoordinates > &coordinates, const OpenSwath::LightTargetedExperiment &transition_exp_used, const bool ms1, const TransformationDescription trafo_inverse, const ChromExtractParams &cp) const
	Function to prepare extraction coordinates that also correctly handles RT transformations. More...
void	prepare_coordinates_sub (std::vector< OpenSwath::ChromatogramPtr > &output_chromatograms, std::vector< ChromatogramExtractorAlgorithm::ExtractionCoordinates > &coordinates, const OpenSwath::LightTargetedExperiment &transition_exp_used, const double rt_extraction_window, const bool ms1) const
	Simple function to prepare extraction coordinates. More...

Protected Attributes
OpenSwath::SpectrumAccessPtr	ms1_map_
	Spectrum Access to the MS1 map (note that this is *not* threadsafe!) More...
bool	use_ms1_traces_
	Whether to use the MS1 traces. More...
Protected Attributes inherited from ProgressLogger
LogType	type_
time_t	last_invoke_
ProgressLoggerImpl *	current_logger_

Private Types
typedef OpenSwath::LightTransition	TransitionType
typedef MRMTransitionGroup< MSChromatogram, TransitionType >	MRMTransitionGroupType

Additional Inherited Members
Public Types inherited from ProgressLogger
enum	LogType { CMD, GUI, NONE }
	Possible log types. More...
Static Protected Member Functions inherited from ProgressLogger
static String	logTypeToFactoryName_ (LogType type)
	Return the name of the factory product used for this log type. More...
Static Protected Attributes inherited from ProgressLogger
static int	recursion_depth_

Detailed Description

Class to execute an OpenSwath Workflow.

The workflow will perform a complete OpenSWATH analysis. Optionally, an RT transformation (mapping peptides to normalized space) can be obtained beforehand using the OpenSwathRetentionTimeNormalization class.

Member Typedef Documentation

MRMTransitionGroupType

typedef MRMTransitionGroup< MSChromatogram, TransitionType> MRMTransitionGroupType

private

TransitionType

typedef OpenSwath::LightTransition TransitionType

private

Constructor & Destructor Documentation

OpenSwathWorkflow()

OpenSwathWorkflow ( bool  use_ms1_traces )

inlineexplicit

References ChromExtractParams::rt_extraction_window.

Member Function Documentation

copyBatchTransitions_()

void copyBatchTransitions_ ( const std::vector< OpenSwath::LightCompound > &  used_compounds, const std::vector< OpenSwath::LightTransition > &  all_transitions, std::vector< OpenSwath::LightTransition > &  output  )

protected

Copy the required transitions to output.

Copy all transitions matching to one of the compounds in the selected peptide vector from all_transitions to the output.

Parameters

used_compounds	Which peptides or metabolites to be used
all_transitions	Transitions vector from which to select transitions
output	Output vector containing matching transitions (taken from all_transitions)

MS1Extraction_()

void MS1Extraction_ ( const std::vector< OpenSwath::SwathMap > &  swath_maps, std::map< std::string, OpenSwath::ChromatogramPtr > &  ms1_chromatograms, Interfaces::IMSDataConsumer *  chromConsumer, const ChromExtractParams &  cp, const OpenSwath::LightTargetedExperiment &  transition_exp, const TransformationDescription &  trafo_inverse, bool  load_into_memory, bool  ms1only = false  )

protected

Perform MS1 extraction and store result in ms1_chromatograms.

performExtraction()

void performExtraction	(	const std::vector< OpenSwath::SwathMap > &	swath_maps,
		const TransformationDescription	trafo,
		const ChromExtractParams &	cp,
		const Param &	feature_finder_param,
		const OpenSwath::LightTargetedExperiment &	transition_exp,
		FeatureMap &	out_featureFile,
		bool	store_features,
		OpenSwathTSVWriter &	tsv_writer,
		OpenSwathOSWWriter &	osw_writer,
		Interfaces::IMSDataConsumer *	chromConsumer,
		int	batchSize,
		bool	load_into_memory
	)

Execute the OpenSWATH workflow on a set of SwathMaps and transitions.

Executes the following operations on the given input:

1. Selecting the appropriate transitions for each SWATH window (using OpenSwathHelper::selectSwathTransitions) 2. Extract the chromatograms from the SWATH maps (MS1 and MS2) using (ChromatogramExtractor) 3. Pick peaks in the chromatograms and perform peak scoring (inside scoreAllChromatograms function) 4. Write out chromatograms and found features

Parameters

swath_maps	The raw data (swath maps)
trafo	Transformation description (translating this runs' RT to normalized RT space)
cp	Parameter set for the chromatogram extraction
feature_finder_param	Parameter set for the feature finding in chromatographic dimension
transition_exp	The set of assays to be extracted and scored
out_featureFile	Output feature map to store identified features
store_features	Whether features should be appended to the output feature map
tsv_writer	TSV Writer object to store identified features in csv format
osw_writer	OSW Writer object to store identified features in SQLite format
chromConsumer	Chromatogram consumer object to store the extracted chromatograms
batchSize	Size of the batches which should be extracted and scored
load_into_memory	Whether to cache the current SWATH map in memory

Referenced by SortPairDoubleByFirst().

prepare_coordinates_sub()

void prepare_coordinates_sub ( std::vector< OpenSwath::ChromatogramPtr > &  output_chromatograms, std::vector< ChromatogramExtractorAlgorithm::ExtractionCoordinates > &  coordinates, const OpenSwath::LightTargetedExperiment &  transition_exp_used, const double  rt_extraction_window, const bool  ms1  ) const

protected

Simple function to prepare extraction coordinates.

This will take the targeted experiment and prepare extraction coordinates (either MS1 or MS2) for extraction by the ChromatogramExtractor.

Parameters

output_chromatograms	Output of chromatograms (will be filled with empty chromatogram ptrs)
coordinates	Output of extraction coordinates (will be filled with matching extraction coordinates)
transition_exp_used	The transition experiment used to create the coordinates
rt_extraction_window	Window for retention time extraction
ms1	Whether extraction coordinates should be created for MS1 (if false, it will be for MS2)

prepareExtractionCoordinates_()

void prepareExtractionCoordinates_ ( std::vector< OpenSwath::ChromatogramPtr > &  chrom_list, std::vector< ChromatogramExtractorAlgorithm::ExtractionCoordinates > &  coordinates, const OpenSwath::LightTargetedExperiment &  transition_exp_used, const bool  ms1, const TransformationDescription  trafo_inverse, const ChromExtractParams &  cp  ) const

protected

Function to prepare extraction coordinates that also correctly handles RT transformations.

Creates a set of (empty) chromatograms and extraction coordinates with the correct ids, m/z and retention time start/end points to be extracted by the ChromatogramExtractor.

Handles rt extraction windows by calculating the correct transformation for each coordinate.

Parameters

chrom_list	Output of chromatograms (will be filled with empty chromatogram ptrs)
coordinates	Output of extraction coordinates (will be filled with matching extraction coordinates)
transition_exp_used	The transition experiment used to create the coordinates
ms1	Whether to perform MS1 (precursor ion) or MS2 (fragment ion) extraction
trafo_inverse	Inverse transformation function
cp	Parameter set for the chromatogram extraction

scoreAllChromatograms()

void scoreAllChromatograms ( const OpenSwath::SpectrumAccessPtr  input, const std::map< std::string, OpenSwath::ChromatogramPtr > &  ms1_chromatograms, const std::vector< OpenSwath::SwathMap >  swath_maps, OpenSwath::LightTargetedExperiment &  transition_exp, const Param &  feature_finder_param, TransformationDescription  trafo, const double  rt_extraction_window, FeatureMap &  output, OpenSwathTSVWriter &  tsv_writer, OpenSwathOSWWriter &  osw_writer, bool  ms1only = false  )

protected

Perform scoring on a set of chromatograms.

Will iterate over all assays contained in transition_exp and for each assay fetch the corresponding chromatograms and find peak groups.

Parameters

input	Input chromatograms (MS2 level)
ms1_chromatograms	Input chromatograms for MS1-level
swath_maps	Set of swath map(s) for the current swath window (for SONAR multiple maps are provided)
transition_exp	The transition experiment (assay library)
feature_finder_param	Parameters for the MRMFeatureFinderScoring
trafo	RT Transformation function
rt_extraction_window	RT extraction window
output	Output map
tsv_writer	TSV writer for storing output (on the fly)
osw_writer	OSW Writer object to store identified features in SQLite format

selectCompoundsForBatch_()

void selectCompoundsForBatch_ ( const OpenSwath::LightTargetedExperiment &  transition_exp_used_all, OpenSwath::LightTargetedExperiment &  transition_exp_used, int  batch_size, size_t  j  )

protected

Select which compounds to analyze in the next batch (and copy to output)

This function will select which compounds to analyze in the next batch j and will copy the corresponding compounds and transitions into the output structure. The output will contain batch_size compounds.

Parameters

transition_exp_used_all	input (all transitions for this swath)
transition_exp_used	output (will contain only transitions for the next batch)
batch_size	how many compounds per batch
j	batch number (peptides from j*batch_size to j*batch_size+batch_size will be copied)

Note

The proteins will be copied completely without checking for a match

writeOutFeaturesAndChroms_()

void writeOutFeaturesAndChroms_ ( std::vector< OpenMS::MSChromatogram > &  chromatograms, const FeatureMap &  featureFile, FeatureMap &  out_featureFile, bool  store_features, Interfaces::IMSDataConsumer *  chromConsumer  )

protected

Write output features and chromatograms to disk.

Member Data Documentation

ms1_map_

OpenSwath::SpectrumAccessPtr ms1_map_

protected

Spectrum Access to the MS1 map (note that this is *not* threadsafe!)

Note

This pointer is not threadsafe, please use the lightClone() function to create a copy for each thread

This pointer may be NULL if use_ms1_traces_ is set to false

use_ms1_traces_

bool use_ms1_traces_

protected

Whether to use the MS1 traces.